Choices
by Xaiban
Summary: AU:Obito kidnaps Kushina and tries to extract the Kyuubi. After he fails, Zetsu tells him that the seal will weaken during child birth. Not knowing if she was involved with anyone he decided to do the deed himself. This story is about the result of this choice.
1. Chapter 1

**Disclaimer: I don't own Naruto or anything else mentioned in this story.**

Kushina Uzumaki was walking home from the market with a soft smile on her face. She was really happy; Kushina had been dating Minato Namikaze for the last six months. Earlier he told her to cook her favorite food for dinner because he had something to talk to her about that would change their lives forever. Naturally when she heard that she thought he was going to propose to her.

Dinner was full of small talk and silent anticipation. When they were done eating, Minato cleared his throat.

"Kushina." She looked deep into his eyes, making sure to remember every detail of this moment.

"Today I was asked to be the Fourth Hokage." It took her a minute to realize what he'd said. Then Kushina gave him the biggest smile she could muster in the face of such massive disappointment.

"That's great news Minato-kun. I can't think of anyone who deserves it more." Thankfully he mistook the tears in her eyes for happiness. He took her hand and led her into their bedroom, to celebrate the way all young couples do. Once they were finished Kushina rolled over and silently cried herself to sleep.

The next evening found Kushina in a bar drinking and sulking. No one bothered her because her temper has quite a reputation of its own. Once she figured she had enough she started to stumble home, not noticing the figure appear behind her.

The figure reached his right hand out hand touched her shoulder, and then they both disappeared into what looked like a black hole.

When Kushina woke the next morning she couldn't remember anything that had happened. When she moved to get up she felt as if she'd been punched in the stomach. Pulling up her shirt she noticed the pain was coming from her seal, the skin around which was red and sore. Worrying that the seal was weakening, she woke Minato up to have him check the seal.

As Minato studied the seal on his girlfriend's stomach he couldn't see anything wrong with the sealing array. He did notice that the skin was irritated so he told her to go to the hospital for a complete check-up. As the day passed the pain and soreness went away, she figured she must have just slept on it wrong, so she decided to forgo the hospital visit. It wasn't until a month and a half later that she had wished she'd gone.

The last couple of days Kushina had been having off and on stomach aches. This brought back fears that her seal was acting up from a month ago. She decided it would be best, no matter how much she hated it, if she went to the hospital for a check-up.

Kushina sat on the hospital bed waiting for the results of her tests to come back. Just as she was getting up to leave; the door opened. A nurse walked in, while looking through Kushina's medical chart, and smiled at her.

"Miss Uzumaki, thank you for waiting we're a little short staffed lately." Kushina nodded that it was okay, although she was annoyed at how long it had taken. "All your tests came back normal and you are fit for active duty. Was there any specific reason you came in today?"

"Well the last few days I've been having sporadic stomach aches." Kushina held her stomach as she said all this.

"That's normal in the early stages of pregnancy it usually goes away after the first trimester. So there's nothing to worry about." The nurse recognized the look on her face. "You didn't know you were pregnant, did you?" Kushina was pale and just shook her head.

The nurse said her congratulations and left so she could have some time to think. Kushina's thoughts were anything from 'Pregnant' to 'How do I tell Minato about this, he just became Hokage.' To say Kushina was scared was an understatement; she remembered when her friend Mikoto Uchiha had Itachi, and all the screaming that came from the delivery room.

-Eight Months Later-

"Push, one last time". The women speaking was Kushina's midwife Biwako Sarutobi. With one last big push, Kushina did as she was told while her husband Minato concentrated on keeping her seal steady. Then the cries of a baby were heard.

"It's a boy." The midwife said. She cut the umbilical cord and moved to wash the child. Minato wasn't able to catch a glimpse of his son before he was taken to be cleaned, and he couldn't move to see him because he had to maintain the seal. After he turned his attention back to the seal he heard the sound a body hitting the floor. He turned to see Biwako dead and a masked man holding his son.

"Step away from the Jinchūriki." The assassin said slowly with a calm tone. He was also holding the baby. "Or the child dies." Once he finished speaking the man threw the baby into the air.

The masked man jump into the air with a knife aimed at the defenseless child's chest. Just before the knife pierced the baby the child disappeared only to reappear on the other side of the room in the hands of the Hokage.

When the man landed he activated the exploding tags he had put on the blanket that was wrapped around the baby. Hearing the hissing of the tag Minato tore the blanket off and jumped with the baby through the door and out into the yard of the cottage. A second later the building exploded.

When he came to a stop he looked down to check on his son. This was the first time he had seen him. The baby had short purple hair and most shockingly was a girl. It was then that it hit him, this wasn't his child. The masked man must have switched him with the girl. Minato quickly hiraishined them to his home and lay her on his bed. Then he went to save Kushina and Naruto, they had decided to name their son after the main character of Minato's sensei's first novel.

He arrived just in time to save Kushina from the nine-tails. Looking around he didn't see Naruto anywhere. So he took Kushina home and then left to deal with the Kyuubi. As Hokage he had to put the village first, his search for Naruto would have to wait.

Minato had just defeated the masked man and asked where Naruto was. The only reply he received was 'There is no Naruto.' As the man disappeared into what appeared to be a vortex Minato heard the Kyuubi Roar and hiraishined to the top of his head on the Hokage Monument. The Kyuubi saw him and fired a Tailed Beast Bomb at the monument. The Hokage was able to setup a space-time barrier which teleported the Tailed Beast Bomb to where it was far enough away from the village not to do any damage.

Then he used his hiraishin to teleport himself and the Kyuubi out of the village. What happened after this is a mystery. All the villagers and shinobi know is that the Fourth Hokage his wife and child died and that the Kyuubi was sealed into a baby girl named Ami.

After he retreated from his fight with the Hokage, Obito Uchiha used his Kamui to return to the hideout in the Mountains Graveyard where he had left the baby with Zetsu. This was the same hideout where Madara had saved Obito. When he landed he walked over to the bed where the child lay and looked down on him.

The boy had short black hair and three whisker shaped birthmarks on each cheek. This child was Obito's son. Nine months ago he had kidnapped the child's mother and tried to remove the Kyuubi from her seal. When he failed Zetsu told him about how the seal would weaken during child birth. Not knowing if she was currently involved with anyone he did the deed himself. The genjutsu he used on her would ensure that she never remembered what happened. Seeing that the child was sleeping peacefully he summoned Zetsu and told him to bring a clone to him.

"You are to copy me and then take him to a nearby civilian village and raise him, his name is Izuna. When I come to get him in a few years I want him to have a strong attachment to me." Obito paused and looked into the Zetsu clones eyes. "You will protect him at all costs. Understood?" Obito growled.

As the clone nodded Obito turned and took a good look at his son. He wished he could raise the boy himself, but until he was able to step back and let Nagato handle everything, he wouldn't have time to think about Izuna. Until then, it was business as usual.

**Thank you for reading. My updating will be rather unpredictable so I don't know when or if this will continue. Thank you again.**


	2. Chapter 2

**Disclaimer: I don't own Naruto**

* * *

-Three Years Later-

It had been three years since Obito had left his son Izuna in the hands of a Zetsu clone. He had monthly updates from Zetsu about his son's safety and condition. Obito was actually a little confused. When he was young he always thought he would be able to stand being away from his family. Growing up an orphan he didn't really know what a family was. He just assumed that the love of family develops over time, since he hadn't spent any time with his son, that's why he doesn't miss him.

Nagato had finally come to meet with Obito. It wouldn't be much longer until he was able to leave most of the work for Nagato to handle. He would have to hurry Izuna's training needed to start in the next few years. Obito had been going nonstop for almost ten years, soon he would be able to relax a bit.

-Two Years Later-

Obito had finally finished teaching Nagato the Rikudō Jutsu. Even though he was a cripple he could now project his will into avatars that he could control. He called them his Six Paths of Pain, they couldn't go too far from Nagato and they each carried only one of the six paths of the Rikudō Jutsu.

Obito was now able to return to the village Izuna was staying in. Zetsu had once asked him why he wanted the boy raised in a civilian village instead of in the hideout. Obito's only reply was that he would need the Mangekyō one day.

Obito appeared from a vortex in front of a small house, which the clone had made with its Mokuton jutsu. It wasn't much just a small two bedroom house a little outside the village. Close enough for Izuna to make friends but far enough for him to train without drawing attention to them.

As Obito walked through the front door he saw a small black haired boy sitting at the kitchen table eating his lunch.

"We'll be starting your training today, after you finish eating." Obito said as he sat opposite the boy at the table. When the boy heard this, his head shot up and he had a gleam in his eye. Izuna had been begging the clone to start his training for months. He knew from a young age that he was one of the few remaining members of the Uchiha Clan.

"Really!" the boy yelled excitedly.

Obito told him to finish eating, and he'd never seen food disappear so fast before. As soon as he was done the boy was standing in the back yard waiting for instructions. While Obito was pleased with his enthusiasm, he would have to calm the boy down or something similar to what happened to him would happen to the boy.

"Okay, first off physical training. It doesn't matter what you know about being a shinobi if you can't move your dead." The boy gulped and nodded. Obito couldn't help but notice the similarities between the two of them. "Run around the edges of the clearing until I tell you to stop." And just like that his training started.

-Five Years later-

Izuna had come far in the last five years. His father had taught him a lot, and though he hadn't activated his sharingan yet, he knew he was strong. Today was his tenth birthday and his father had promised him something really special as a gift.

As Izuna was finishing up his morning workout, he noticed someone was watching him. The man's skin was completely white. The only color Izuna could see was his green hair. When the man noticed he'd been spotted he ran at the boy with a kunai in his right hand.

Izuna saw the kunai and thought of calling for his father, but he had never fought someone other than his dad and wanted to test his strength. He would impress his father by dealing with this guy by himself.

The man swung the kunai at the boy's throat; the boy leaned back and kicked him in the stomach. The man caught his foot and threw Izuna into a nearby tree. Izuna flew through the air and his right shoulder hit a tree. There was a loud snap and Izuna screamed. His shoulder was dislocated.

Lying on the ground, feeling real pain for the first time in his life, he was a little disoriented. He had been injured in his spars with his father but he'd never broken any bones. He was wondering where his dad was, surely he heard him scream, they weren't that far from the house.

'Maybe he killed dad first.' Izuna thought starting to panic. 'I have to get up, keep fighting.'

Izuna stood up holding his right arm with his left. His attacker pulled his right arm back and threw the kunai. Izuna dodged to left into the path of another kunai he hadn't noticed. The kunai struck his left shoulder, and his arm dropped limp.

The man charged ahead at full speed with another kunai in hand. Izuna turned and ran toward the house. Dodging the kunai his attacker was throwing, one he missed sliced through the back of his right knee. Izuna collapsed and rolled onto his back, the man was still charging.

All Izuna could do was sit and watch as his would be killer drew nearer. When the man was only ten feet away things changed. His vision sharpened and the man's movements seemed to slow down a little bit.

As the kunai was swinging down to take Izuna's life the man looked him in the eye. As the boy was closing his eyes Zetsu noticed that the boy had unlocked his sharingan. Zetsu stopped the kunai.

When Izuna noticed the lack of pain he slowly opened his eyes. He saw his attacker standing a few feet away from him smiling at him. Then his father appeared using his Kamui.

"Happy birthday Izuna-kun." Said the man who attacked him. Izuna just stared at him like he was crazy.

"Yes, happy birthday. My gift to you was your first true taste of combat against an enemy attacking with killing intent." Izuna was baffled his father had set all this up. "You also unlocked your sharingan. Now your real training can begin." And begin his training did, nothing he'd done before this was near as intense.

By the time Izuna was twelve his father had him hunting B-Rank Missing Nins for combat experience. His father told him that soon he would be ready for the next level of the sharingan. This surprised Izuna because he'd never known there was another level.

Now he was about to go on his first mission with his father. They were going to collect the bounty on Sharingan no Kakashi an A-Rank Shinobi from Konoha. Zetsu reported that Kakashi was taking his team of genin on a C-Rank mission to wave country. This was going to be fun.

* * *

**Chapter two is done next chapter will feature Izuna and Obito against Kakashi and his Genin. I don't have a beta or know how to get one so I apologize for errors.**


	3. Chapter 3

**Disclaimer: I don't own Naruto.**

* * *

It was early when Izuna and his father appeared in Wave Country. Izuna had traveled this way several times but it still felt weird.

As they were walking through the village Izuna noticed that while it was run down the villagers all seemed happy. Everyone was smiling and children were running in the streets. He was starting to wonder if Zetsu's information had been wrong. Wave Country was supposed to be quite and everyone was supposed to be afraid. So why now then were they so happy?

Obito told Izuna to scout around for information on Kakashi's location. People were more likely to talk to a curious child then an intimidating adult. Izuna went and started playing with the other kids his age, while subtly asking questions about the Konoha shinobi and why everyone was so happy.

Apparently during the mission, which was already over, the warlord who they all feared had been killed. Once he heard that Kakashi and his genin had already left, he went to find his father who just happened to be having a drink.

It wasn't long before Zetsu returned with the location of where Kakashi had made his camp for the night. Kakashi had first watch so they chose to wait a few hours before going in.

They appeared silently one mile away from the campsite. They slowly made their way forward when suddenly Obito threw a kunai at a dog that was wearing a bandana with the Konoha symbol on it. One of Kakashi's summons.

Uchiha Sasuke was sitting at the foot of a tree thinking of ways to increase his strength when he heard a 'poof' and then a 'thunk' in rapid succession. Having trained for years Sasuke immediately recognized the sound of a kunai hitting a tree. He sprang to his feet and rushed to Kakashi's tent.

As Obito and Izuna were approaching the campsite they saw a black haired boy about Izuna's age run into a tent and returned a few seconds later with Kakashi in tow. The boy went to the other tents and woke up his teammates.

They stopped when they were about forty feet from Kakashi. Doing as his father had taught him Izuna kept his face completely emotionless. Kakashi stood with two genin on his right and another on his left. On the right was the black haired boy that woke Kakashi and next to him was a pink haired girl who looked like she was about to faint from fright. On Kakashi's left there was a purple haired girl who looked ready for a fight.

"Sharingan no Kakashi, you have quite a bounty." Obito said. "It will fill my wallet well. I won't have to hunt anyone else for months."

Kakashi whispered some orders to his team and then lifted his headband. His sharingan was able to pick up details in the dark that his regular eye had missed. The most shocking thing he noticed was that both of the shinobi in front of him had fully developed sharingan, even though the man only had one sharingan. He knew Sasuke's one tomoe sharingan wouldn't hold up against the other boys three tomoe.

"I want you three to stay out of this fight." Kakashi spoke to his genin while not taking his eyes the enemy. "They are above your level." This obviously damaged the young Uchiha's pride, seeing another boy his age that was stronger than he was.

"I have my sharingan now, he can't defeat me." Sasuke said before he charged at Izuna.

Kakashi moved to stop Sasuke but he had to dodge a kick from the masked man.

"Don't worry about him, he won't be hurt. There are so few of us Uchiha left it would be a shame to see one die." Obito had told Izuna prior to the fight that he had plans that involved two of the genin on this team. He could hurt them but he couldn't kill them.

-With Izuna and Sasuke-

They were currently engaged in a taijutsu battle that left Izuna a little disappointed. Zetsu said the boy was considered a prodigy in Konoha. If this is what passed for a prodigy in Konoha then the standards must have fallen far from what they were when his father had lived there.

Sasuke was giving everything he had but he couldn't land a hit no matter what he tried. Sometimes he would notice that his enemy was moving to block before he had even threw a punch or kick. It was like fighting Kakashi for the bell all over again.

Sasuke back flipped a good distance away and made the hand seals for the Grand Fire Ball jutsu.

Izuna dodged the jutsu, withdrew a kunai and threw it at Sasuke.

Sasuke rolled to the right and had to keep dodging as there were six small fireballs flying toward him.

Seeing Sasuke in trouble his teammates moved to help. The purple haired girl charged while the pink one threw a kunai with an exploding tag tied to the handle. Izuna withdrew a kunai and deflected the incoming projectile toward the charging girl. She immediately ducked and the kunai passed harmlessly over her body where it hit a tree and detonated.

Izuna was about to comment on their lack of skill when he heard a loud screeching noise followed by the sound of something penetrating flesh. Izuna turned to see Kakashi had a lightning covered arm stuck through his father's chest.

"Dad!" Izuna yelled as he ran toward his father.

When Kakashi heard what the boy had called the man he felt immense sorrow for the boy. He himself had found his father's body after he committed suicide. But even he couldn't imagine watching him die. As the boy ran toward them Kakashi pulled his arm out of the man's chest and jumped away so the boy could have his final moments with his father in piece.

"Dad! Why?" Izuna cried kneeling beside his dying father. Izuna was confused. He didn't understand why his father hadn't used his Kamui to escape if the fight was too much for him. Why would he just stand there and die?

"Because you needed it." Obito said lifting a finger and tapping Izuna just under his left eye. "The Mangekyō is your now. Learn to wield it as well as Madara and you will bring honor back to our clan." As Obito spoke his hand began to fall, when he had finished he lay unmoving. Izuna stayed there kneeling over his father's body for another minute before standing up and turning to Kakashi.

Kakashi watched as the boy stood and turned to him, with his head lowered. He wasn't sure if the boy would attack or run, but he knew he had to take the boy back to Konoha. When the elders and the council hear that there is an Uchiha living outside the village and that Kakashi had let him go he could be tried for treason.

The boy raised his head and settled a glare that connected with Kakashi's sharingan. In that moment all the hatred seemed to fade away and was replaced with a feeling of peace and Izuna started to dose off.

Izuna realized that Kakashi had used his sharingan to put him under a genjutsu. As soon as he noticed this he activated his own sharingan and the genjutsu was canceled. However just after escaping from the genjutsu he was chopped in the neck by a shadow clone Kakashi had created while Izuna was still mourning.

The last thing Izuna remembered was hearing Kakashi say "I'm sorry" before the light faded.

When the boy dropped to the ground Kakashi looked over to see that his team was okay. This wasn't the first time they had seen someone die so he knew they would be okay with this. Kakashi could tell by the look in Sasuke's eye that he was upset that he'd been beaten by another boy his age for the second time in two weeks.

With a sigh Kakashi told them to pack up camp, they needed to leave soon. Kakashi's shadow clone started digging a grave for the man while Kakashi watched the boy. He didn't notice a pale skinned man, with green hair and a smirk on his face, peaking around a tree before sinking into the ground.

-With Zetsu-

Zetsu rose from the ground at the hideout in the Mountains Graveyard. Looking around he saw Obito sitting on Madara's throne, where he'd been waiting for Zetsu.

"Well?" Obito said.

"Everything went as planned the clone died, Izuna acquired the Mangekyō and Kakashi is taking him to Konoha." Zetsu explained. "I still don't see why he couldn't stay here while you were gone."

"Because, he still needs training. Training that you cannot give him and I have to go and make sure that Nagato hasn't screwed everything up." Obito explained. He was rather annoyed that he had to explain this again. "Once things have calmed down a little and he isn't being watched so closely you will go and explain everything to him."

"Oh yeah, I keep forgetting that part." Zetsu said while sinking back into the ground. "I will return and let know when it is done."

* * *

**Well that's chapter three. I wanted to write a fight scene with Kakashi and Obito but I couldn't think of a way to make that work. I mean Zetsu clones are pretty weak so that just wouldn't make sense having Kakashi going all out on one.**

**I want to let you readers know that Izuna will not be a Konoha shinobi he might "join" Konoha but he'll leave as soon as Zetsu and Obito tell him too. Its all a part Obito's plan. Thanks for reading.**


End file.
